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How does TCGA get Segment_Mean in files of copy number variations?

Hi all,

I have download the copy number variation file of Ovarian serous cystadenocarcinoma in TCGA.

How does TCGA get Segment_Mean (please see the following image) in the of copy number variations files? Is there any algorithm to calculate the Segment_Mean? What is the algorithm?

enter image description here

The file shown in the above image was downloaded in: https://gdc-portal.nci.nih.gov/search/s

The following image show the position where the file was downloaded:

enter image description here

Thanks for any help.

snp sequencing sequence
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updated by EagleEye EagleEye • written by Ashleyca • Ashleyca

1 answer

These were calculated via CBS algorithm using tangent copy number data. The tangent data is derived from Birdsuite package from Affy SNP6 array.

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written by Zhenyu Zhang Zhenyu Zhang

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